Related papers: Theoretical investigation of finite size effects a…
The distance distribution between complementary base pairs of the two strands of a DNA molecule is studied near the melting transition. Scaling arguments are presented for a generalized Poland-Scheraga type model which includes…
Conformational change of a DNA molecule is frequently observed in multiple biological processes and has been modelled using a chain of strongly coupled oscillators with a nonlinear bistable potential. While the mechanism and properties of…
Reduced large N gauge theories have a phase with unbroken center symmetry and phases in which that symmetry is broken for Polyakov loops in one or more lattice directions. The phase with unbroken symmetry is associated with the zero…
This study investigates in detail the finite-size scaling of the two-dimensional irrationally frustrated XY model. By means of Monte Carlo simulations with entropic sampling, we examine the size dependence of the specific heat, and find…
The zero-temperature transmission rate spectrum of a double-chain tight-binding model for real DNA is calculated. It is shown that a band of extended-like states exists only for finite chain length with strong inter-chain coupling. While…
Quantum phase transitions occur when quantum fluctuation destroys order at zero temperature. With an increase in temperature, normally the thermal fluctuation wipes out any signs of this transition. Here we identify a physical quantity that…
The effect of defects on the melting profile of short heterogeneous DNA chains are calculated using the Peyrard-Bishop Hamiltonian. The on-site potential on a defect site is represented by a potential which has only the short-range…
We numerically study the finite-size droplet condensation-evaporation transition in two dimensions. We consider and compare two orthogonal approaches, namely at fixed temperature and at fixed density, making use of parallel multicanonical…
The phase transition in the q-state Potts model with homogeneous ferromagnetic couplings is strongly first order for large q, while is rounded in the presence of quenched disorder. Here we study this phenomenon on different two-dimensional…
The thermodynamic properties of DNA circular molecules are investigated by a new path integral computational method which treats in the real space the fundamental forces stabilizing the molecule. The base pair and stacking contributions to…
Understanding how monomeric proteins fold under in vitro conditions is crucial to describing their functions in the cellular context. Significant advances both in theory and experiments have resulted in a conceptual framework for describing…
Complementary strands in DNA double helix show temporary fluctuational openings which are essential to biological functions such as transcription and replication of the genetic information. Such large amplitude fluctuations, known as the…
Zero mode waveguide technology of next generation sequencing demonstrated sequence-dependence of the enzymatic reaction, incorporating a base into the genomic DNA. We show that these experimental results indicate existence of a previously…
We study the folding of RNA secondary structures with quenched sequence randomness by means of the constrained annealing method. A thermodynamic phase transition is induced by including the conformational weight of loop structures. In…
Using free-fermionic techniques we study the entanglement entropy of a block of contiguous spins in a large finite quantum Ising chain in a transverse field, with couplings of different types: homogeneous, periodically modulated and random.…
Pinning models are built from discrete renewal sequences by rewarding (or penalizing) the trajectories according to their number of renewal epochs up to time $N$, and $N$ is then sent to infinity. They are statistical mechanics models to…
We present a detailed study of the finite temperature dynamical properties of the quantum Potts model in one dimension.Quasiparticle excitations in this model have internal quantum numbers, and their scattering matrix {\gf deep} in the…
We present a comprehensive theoretical study of finite size effects in the relaxation dynamics of glass-forming liquids. Our analysis is motivated by recent theoretical progress regarding the understanding of relevant correlation length…
We show numeric evidence that, at low enough temperatures, the potential energy density of a glass-forming liquid fluctuates over length scales much larger than the interaction range. We focus on the behavior of translationally invariant…
Test experiments of hybridization in DNA microarrays show systematic deviations from the equilibrium isotherms. We argue that these deviations are due to the presence of a partially hybridized long-lived state, which we include in a kinetic…